Hi again, 

I got this with "hg heads" : 

changeset: 7986:12fcd068b12e 
tag: tip 
user: Daniel Blankenberg <d...@bx.psu.edu> 
date: Thu Oct 18 11:22:12 2012 -0400 
summary: Do not hide failed datasets with HideDatasetAction post job action. 

changeset: 7152:ffc20445b35e 
branch: split_blast2 
parent: 7058:22f545c0d412 
user: Dannon Baker <dannonba...@me.com> 
date: Wed Apr 18 07:59:38 2012 -0400 
summary: Branch close. 

changeset: 7151:c94957ac5454 
branch: workflow_import_menu_api 
parent: 6834:1a3d01b09f7a 
user: Dannon Baker <dannonba...@me.com> 
date: Wed Mar 21 09:50:44 2012 -0400 
summary: Branch close for pull request. 

changeset: 7150:314a10ae112d 
branch: split_blast 
parent: 6757:ebf65c0b1e26 
user: Dannon Baker <dannonba...@me.com> 
date: Tue Feb 28 12:32:54 2012 -0500 
summary: Close split_blast branch 

changeset: 7149:1327f2219423 
branch: meme_requirement_on_fimo 
parent: 6662:8ba74c17e809 
user: Daniel Blankenberg <d...@bx.psu.edu> 
date: Fri Feb 03 11:15:29 2012 -0500 
summary: close branch 
-------------------------------------------------------- 

And I got this with the debug at : 

JSONDecodeError: Unterminated string starting at: line 1 column 65522 (char 
65522) 

URL: http://dev-galaxy.genouest.org/admin_toolshed/browse_repositories 
File 
'/opt/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
 line 364 in respond 
app_iter = self.application(environ, detect_start_response) 
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 
in __call__ 
environ, self.app) 
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in 
intercept_output 
app_iter = application(environ, replacement_start_response) 
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in 
__call__ 
return self.application(environ, start_response) 
File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 
91 in __call__ 
return self.app( environ, start_response ) 
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 
632 in __call__ 
return self.application(environ, start_response) 
File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ 
body = method( trans, **kwargs ) 
File '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 203 in 
decorator 
return func( self, trans, *args, **kwargs ) 
File '/opt/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 381 
in browse_repositories 
return self.installed_repository_grid( trans, **kwd ) 
File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 277 in 
__call__ 
kwargs=kwargs ) 
File '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 765 in 
fill_template 
return self.fill_template_mako( filename, **kwargs ) 
File '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 776 in 
fill_template_mako 
return template.render( **data ) 
File '/opt/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in 
render 
return runtime._render(self, self.callable_, args, data) 
File '/opt/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in 
_render 
**_kwargs_for_callable(callable_, data)) 
File '/opt/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in 
_render_context 
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs) 
File '/opt/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in 
_exec_template 
callable_(context, *args, **kwargs) 
File '/opt/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in 
render_body 
__M_writer(unicode(next.body())) 
File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 119 
in render_body 
__M_writer(unicode(self.grid_body( grid ))) 
File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 784 
in render_grid_body 
__M_writer(unicode(self.make_grid( grid ))) 
File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 813 
in render_make_grid 
__M_writer(unicode(self.render_grid_table( grid, show_item_checkboxes ))) 
File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 762 
in render_render_grid_table 
__M_writer(unicode(render_grid_table_body_contents( grid, show_item_checkboxes 
))) 
File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 658 
in render_grid_table_body_contents 
return 
render_render_grid_table_body_contents(context,grid,show_item_checkboxes) 
File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 281 
in render_render_grid_table_body_contents 
for i, item in enumerate( query ): 
File 
'/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py',
 line 1422 in instances 
rows = [process[0](context, row) for row in fetch] 
File 
'/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py',
 line 2032 in main 
return _instance(row, None) 
File 
'/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/mapper.py',
 line 1729 in _instance 
populate_state(state, dict_, row, isnew, only_load_props) 
File 
'/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/mapper.py',
 line 1614 in populate_state 
populator(state, dict_, row, isnew=isnew, **flags) 
File 
'/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/strategies.py',
 line 120 in new_execute 
dict_[key] = row[col] 
File 
'/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py',
 line 1348 in __getitem__ 
return self.__parent._get_col(self.__row, key) 
File 
'/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py',
 line 1620 in _get_col 
return processor(row[index]) 
File 
'/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/types.py',
 line 284 in process 
return self.process_result_value(impl_processor(value), dialect) 
File '/opt/galaxy-dist/lib/galaxy/model/custom_types.py', line 50 in 
process_result_value 
return json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) ) 
File 
'/opt/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/decoder.py',
 line 402 in decode 
File 
'/opt/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/decoder.py',
 line 418 in raw_decode 
JSONDecodeError: Unterminated string starting at: line 1 column 65522 (char 
65522) 
---------------------------------------------- 

I hope this can help you find the problem ! 

Thanks, 
Mathieu 

----- Mail original -----

> De: "Greg Von Kuster" <g...@bx.psu.edu>
> À: "Mathieu Bahin" <mathieu.ba...@irisa.fr>
> Cc: galaxy-...@bx.psu.edu
> Envoyé: Lundi 12 Novembre 2012 12:33:10
> Objet: Re: [galaxy-dev] Bug report : JSONDecodeError

> Hi Matthiew,

> Can you clarify the version of Galaxy you are using? What is the
> result of typing "hg heads" in your Galaxy installation directory?

> ALso, I noticed the following in your paster log:

> ----------------------------------------
> 131.254.16.26 - - [12/Nov/2012:10:52:26 +0200] "GET
> /admin_toolshed/browse_repositories HTTP/1.1" 500 - "
> http://dev-galaxy.genouest.org/admin " "Mozilla/5.0 (X11; Linux
> x86_64; rv:12.0) Gecko/20100101 Firefox/12.0"
> Debug at: http://dev-galaxy.genouest.org/_debug/view/1352713905

> Directing your browser to the URL in the "Debug at" address will
> provide a stack trace of the exception thrown due to the problem.
> What is this this complete stack trace?

> Thanks,

> Greg Von Kuster

> On Nov 12, 2012, at 4:56 AM, Mathieu Bahin wrote:

> > And here is the paster...
> 

> > ----- Mail original -----
> 

> > > De: "Mathieu Bahin" < mathieu.ba...@irisa.fr >
> > 
> 
> > > À: "Greg Von Kuster" < g...@bx.psu.edu >
> > 
> 
> > > Cc: galaxy-...@bx.psu.edu
> > 
> 
> > > Envoyé: Lundi 12 Novembre 2012 10:54:21
> > 
> 
> > > Objet: Re: [galaxy-dev] Bug report : JSONDecodeError
> > 
> 

> > > Hi Greg !
> > 
> 

> > > Thanks for the quick answer.
> > 
> 

> > > I am using the 7720 parent version but I keep it up-to-date
> > > without
> > > any problems.
> > 
> 
> > > Enclosed you'll find the 'paster.log' file generated when I start
> > > Galaxy and try to access the manage installed tool shed
> > > repositories
> > > page.
> > 
> 

> > > Cheers,
> > 
> 
> > > Mathieu Bahin
> > 
> 

> > > ----- Mail original -----
> > 
> 

> > > > De: "Greg Von Kuster" < g...@bx.psu.edu >
> > > 
> > 
> 
> > > > À: "Mathieu Bahin" < mathieu.ba...@irisa.fr >
> > > 
> > 
> 
> > > > Cc: galaxy-...@bx.psu.edu
> > > 
> > 
> 
> > > > Envoyé: Vendredi 9 Novembre 2012 19:28:09
> > > 
> > 
> 
> > > > Objet: Re: [galaxy-dev] Bug report : JSONDecodeError
> > > 
> > 
> 

> > > > Hello Mathieu,
> > > 
> > 
> 

> > > > What version of Galaxy are you running? Also, I cannot read the
> > > > stack
> > > > trace from your pasted image, so can you send a text version of
> > > > the
> > > > complete stack trace from your paster log?
> > > 
> > 
> 

> > > > Thanks,
> > > 
> > 
> 

> > > > Greg Von Kuster
> > > 
> > 
> 

> > > > On Nov 9, 2012, at 11:26 AM, Mathieu Bahin wrote:
> > > 
> > 
> 

> > > > > Hi,
> > > > 
> > > 
> > 
> 

> > > > > I am using my own Galaxy instance and I had a problem
> > > > > removing
> > > > > a
> > > > > tool
> > > > > from the tool shed : mothur.
> > > > 
> > > 
> > 
> 
> > > > > The installation was ok and I the mothur tool running without
> > > > > any
> > > > > problem. But when I tried to uninstall the tool, I get an
> > > > > error
> > > > > (screenshot enclosed). And I get the same every time I try to
> > > > > go
> > > > > on
> > > > > the 'Manage tool shed repositories' in the Admin panel.
> > > > 
> > > 
> > 
> 

> > > > > I have tried to rebuilt the eggs and to restart Galaxy
> > > > > basically.
> > > > > Actually, I don't really understand the error message.
> > > > 
> > > 
> > 
> 

> > > > > Cheers,
> > > > 
> > > 
> > 
> 
> > > > > Mathieu Bahin
> > > > 
> > > 
> > 
> 
> > > > > <07.png>
> > > > > ___________________________________________________________
> > > > 
> > > 
> > 
> 
> > > > > Please keep all replies on the list by using "reply all"
> > > > 
> > > 
> > 
> 
> > > > > in your mail client. To manage your subscriptions to this
> > > > 
> > > 
> > 
> 
> > > > > and other Galaxy lists, please use the interface at:
> > > > 
> > > 
> > 
> 

> > > > > http://lists.bx.psu.edu/
> > > > 
> > > 
> > 
> 
> > <paster.log>
>
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